@manual{Allaire2018,
annote = {R package version 1.10},
author = {Allaire, J J and Xie, Yihui and McPherson, Jonathan and Luraschi, Javier and Ushey, Kevin and Atkins, Aron and Wickham, Hadley and Cheng, Joe and Chang, Winston},
title = {{rmarkdown: Dynamic Documents for R}},
url = {https://cran.r-project.org/package=rmarkdown},
year = {2018}
}
@techreport{Anderson2016,
author = {Anderson, Robert P and Ara{\'{u}}jo, Miguel and Guisan, Antoine and Lobo, Jorge M and Mart{\'{i}}nez-Meyer, Enrique and Peterson, Townsend and Sober{\'{o}}n, Jorge},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2016{\_}Anderson et al.{\_}Unknown.pdf:pdf},
institution = {GBIF},
pages = {27pp},
title = {{Final Report of the Task Group on GBIF Data Fitness for Use in Distribution Modelling - Are species occurrence data in global online repositories fit for modeling species distributions? The case of the Global Biodiversity Information Facility (GBIF)}},
year = {2016}
}
@manual{Arel-Bundock2018,
annote = {R package version 1.00.0},
author = {Arel-Bundock, Vincent},
title = {{countrycode: Convert Country Names and Country Codes}},
url = {https://cran.r-project.org/package=countrycode},
year = {2018}
}
@article{Beck2013,
author = {Beck, Jan and Ballesteros-Mejia, Liliana and Nagel, Peter and Kitching, Ian J},
doi = {10.1111/ddi.12083},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2013{\_}Beck et al.{\_}Diversity and Distributions.pdf:pdf},
journal = {Divers Distrib},
keywords = {climatic niche space,gbif,global biodiversity information facility,lepidoptera,natural history collections,range extent,range filling,sphingidae},
pages = {1043--1050},
title = {{Online solutions and the 'Wallacean shortfall': what does GBIF contribute to our knowledge of species ' ranges ?}},
volume = {19},
year = {2013}
}
@misc{BGCI-BotanicGardensConservationInternational2017,
author = {BGCI},
title = {{Botanic Gardens Conservation International}},
url = {https://www.bgci.org/},
urldate = {2017-11-20},
year = {2017}
}
@book{bivand2013,
author = {Bivand, Roger S and Pebesma, Edzer and Gomez-Rubio, Virgilio},
publisher = {Springer},
title = {{Applied spatial data analysis with R, Second edition}},
year = {2013}
}
@manual{Bivand2017,
annote = {R package version 0.9-1},
author = {Bivand, Roger and Lewin-Koh, Nicholas},
title = {{maptools: Tools for Reading and Handling Spatial Objects}},
url = {https://cran.r-project.org/package=maptools},
year = {2017}
}
@manual{Bivand2018,
annote = {R package version 0.3-28},
author = {Bivand, Roger and Rundel, Colin},
title = {{rgeos: Interface to Geometry Engine - Open Source ('GEOS')}},
url = {https://cran.r-project.org/package=rgeos},
year = {2018}
}
@misc{CentralIntelligenceAgency2014,
author = {{Central Intelligence Agency}},
title = {{The World Factbook}},
url = {https://www.cia.gov/library/publications/the-world-factbook/},
year = {2014}
}
@manual{Chamberlain2017,
annote = {R package version 0.9.9},
author = {Chamberlain, Scott},
title = {{rgbif: Interface to the Global 'Biodiversity' Information Facility API}},
url = {https://cran.r-project.org/package=rgbif},
year = {2017}
}
@manual{Chamberlain2016,
annote = {R package version 0.1.1},
author = {Chamberlain, Scott},
title = {{scrubr: Clean Biological Occurrence Records}},
url = {https://cran.r-project.org/package=scrubr},
year = {2016}
}
@techreport{Chapman2005,
address = {Copenhagen},
author = {Chapman, Arthur D},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2005{\_}Chapman{\_}Unknown(2).pdf:pdf},
institution = {GBIF},
keywords = {data cleaning,data cleansing},
pages = {58pp},
title = {{Principles and methods of data cleaning - primary species and species occurrence data, version 1.0. Report for the Global Biodiversity Information Facility, Copenhagen.}},
year = {2005}
}
@techreport{Chapman2005,
address = {Copenhagen},
author = {Chapman, Arthur D},
institution = {GBIF},
keywords = {data cleaning,data cleansing},
pages = {58pp},
title = {{Principles and methods of data cleaning - Primary Species and Species Occurrence Data, version 1.0. Report for the Global Biodiversity Information Facility, Copenhagen.}},
year = {2005}
}
@manual{CodebyRichardA.Becker2017,
annote = {R package version 3.2.0},
author = {{code by Richard A. Becker}, Original S and {version by Ray Brownrigg. Enhancements by Thomas P Minka}, Allan R Wilks. R and Deckmyn., Alex},
title = {{maps: Draw Geographical Maps}},
url = {https://cran.r-project.org/package=maps},
year = {2017}
}
@article{Dauby2016,
author = {Dauby, Gilles and Zaiss, Rainer and Blach-Overgaard, Anne and Catarino, Lu{\'{i}}s and Damen, Theo and Deblauwe, Vincent and Dessein, Steven and Dransfield, John and Droissart, Vincent and Duarte, Maria Cristina and Engledow, Henry and Fadeur, Geoffrey and Figueira, Rui and Gereau, Roy E and Hardy, Olivier J and Harris, David J and de Heij, Janneke and Janssens, Steven and Klomberg, Yannick and Ley, Alexandra C and Mackinder, Barbara A and Meerts, Pierre and van de Poel, Jeike L and Sonk{\'{e}}, Bonaventure and Sosef, Marc SM and St{\'{e}}vart, Tariq and Stoffelen, Piet and Svenning, Jens-Christian and Sepulchre, Pierre and can der Burgt, Xander and Wieringa, Jan J and Couvreur, Thomas LP},
doi = {10.3897/phytokeys.74.9723},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2016{\_}Dauby et al.{\_}PhytoKeys.pdf:pdf},
journal = {PhytoKeys},
pages = {1--18},
title = {{RAINBIO: a mega-database of tropical African vascular plants distributions}},
volume = {18},
year = {2016}
}
@article{Diaz2016,
author = {D{\'{i}}az, Sandra and Kattge, Jens and Cornelissen, Johannes H C and Wright, Ian J and Lavorel, Sandra and Dray, St{\'{e}}phane and Reu, Bj{\"{o}}rn and Kleyer, Michael and Wirth, Christian and Prentice, I Colin and Garnier, Eric and B{\"{o}}nisch, Gerhard and Westoby, Mark and Poorter, Hendrik and Reich, Peter B and Moles, Angela T and Dickie, John and Gillison, Andrew N and Zanne, Amy E and Pierce, Simon and Shipley, Bill and Kirkup, Donald and Casanoves, Fernando and Joswig, Julia S and G{\"{u}}nther, Angela and Falczuk, Valeria and R{\"{u}}ger, Nadja and Mahecha, Miguel D and Gorn{\'{e}}, Lucas D},
doi = {10.1038/nature16489},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2016{\_}D{\'{i}}az et al.{\_}Nature.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
number = {7585},
pages = {167--171},
publisher = {Nature Publishing Group},
title = {{The global spectrum of plant form and function}},
volume = {529},
year = {2016}
}
@article{Diaz2016,
author = {D{\'{i}}az, Sandra and Kattge, Jens and Cornelissen, Johannes H C and Wright, Ian J and Lavorel, Sandra and Dray, St{\'{e}}phane and Reu, Bj{\"{o}}rn and Kleyer, Michael and Wirth, Christian and Prentice, I Colin and Garnier, Eric and B{\"{o}}nisch, Gerhard and Westoby, Mark and Poorter, Hendrik and Reich, Peter B and Moles, Angela T and Dickie, John and Gillison, Andrew N and Zanne, Amy E and Pierce, Simon and Shipley, Bill and Kirkup, Donald and Casanoves, Fernando and Joswig, Julia S and G{\"{u}}nther, Angela and Falczuk, Valeria and R{\"{u}}ger, Nadja and Mahecha, Miguel D and Gorn{\'{e}}, Lucas D},
doi = {10.1038/nature16489},
issn = {0028-0836},
journal = {Nature},
number = {7585},
pages = {167--171},
publisher = {Nature Publishing Group},
title = {{The global spectrum of plant form and function}},
volume = {529},
year = {2016}
}
@article{Garcia-Rosello2013,
author = {Garc{\'{i}}a-Rosell{\'{o}}, Emilio and Guisande, C and Gonz, Jacinto and Heine, Juergen and Pelayo-Villamil, Patricia and {Manjarr{\'{e}}s Hernand{\'{e}}z}, Ana and Vaamonde, Antonio and Granado-Lorencio, Carlos},
doi = {10.1111/j.1600-0587.2013.00374.x},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2013{\_}Garc{\'{i}}a-Rosell{\'{o}} et al.{\_}Ecography.pdf:pdf},
journal = {Ecography (Cop)},
pages = {1202--1207},
title = {{ModestR: a software tool for managing and analyzing species distribution map databases}},
volume = {36},
year = {2013}
}
@article{Garcia-rosello2015,
author = {Garc{\'{i}}a-Rosell{\'{o}}, Emilio and Guisande, C{\'{a}}stor and Manjarr{\'{e}}s-hern{\'{a}}ndez, Ana and Gonz{\'{a}}lez-dacosta, Jacinto and Heine, Juergen and Pelayo-villamil, Patricia and Gonz{\'{a}}lez-vilas, Luis and Vari, Richard P and Vaamonde, Antonio and Granado-lorencio, Carlos and Lobo, Jorge M},
doi = {10.1111/geb.12260},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2015{\_}Garc{\'{i}}a-Rosell{\'{o}} et al.{\_}Global Ecology and Biogeography.pdf:pdf},
journal = {Glob Ecol Biogeogr},
keywords = {2014 john wiley,distribution models,gbif,macroecological patterns,marine fishes,point-to-grid,range maps,rapoport,rule,sons ltd},
pages = {335--347},
title = {{Can we derive macroecological patterns from primary Global Biodiversity Information Facility data?}},
volume = {24},
year = {2015}
}
@article{Garcia-rosello2015a,
author = {Garc{\'{i}}a-rosell{\'{o}}, Emilio and Guisande, C{\'{a}}stor and Manjarr{\'{e}}s-hern{\'{a}}ndez, Ana and Gonz{\'{a}}lez-dacosta, Jacinto and Heine, Juergen and Pelayo-villamil, Patricia and Gonz{\'{a}}lez-vilas, Luis and Vari, Richard P and Vaamonde, Antonio and Granado-lorencio, Carlos and Lobo, Jorge M},
doi = {10.1111/geb.12260},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2015{\_}Garc{\'{i}}a-rosell{\'{o}} et al.{\_}Unknown.pdf:pdf},
keywords = {2014 john wiley,distribution models,gbif,macroecological patterns,marine fishes,point-to-grid,range maps,rapoport,rule,sons ltd},
pages = {335--347},
title = {{Can we derive macroecological patterns from primary Global Biodiversity Information Facility data ?}},
year = {2015}
}
@misc{GBIF,
author = {GBIF},
doi = {10.15468/dl.wquvxb},
title = {{Magnoliopsida}},
year = {2017}
}
@misc{GeoNames2017,
author = {GeoNames},
title = {www.geonames.org},
year = {2017}
}
@misc{GeoNames2017,
author = {GeoNames},
title = {www.geonames.org},
year = {2017}
}
@misc{GeoNames2017,
author = {GeoNames},
title = {www.geonames.org},
year = {2017}
}
@misc{GlobalBiodiveristyInformationFacility2017,
author = {{Global Biodiveristy Information Facility}},
title = {{List of data publishers}},
url = {www.gbif.org/publisher/search},
year = {2017}
}
@misc{GBIF,
author = {{Global Biodiveristy Information Facility}},
doi = {10.15468/dl.wquvxb},
title = {{Magnoliopsida}},
url = {www.gbif.org},
urldate = {2017-02-02},
year = {2017}
}
@misc{GBIF,
author = {{Global Biodiveristy Information Facility}},
doi = {10.15468/dl.wquvxb},
title = {{Magnoliopsida}},
url = {www.gbif.org},
year = {2017}
}
@misc{GoogleInc2017,
author = {{Google Inc}},
title = {{Google Earth Pro, 7.1.7.2606}},
year = {2017}
}
@article{Graham2008,
author = {Graham, Catherine H and Elith, Jane and Hijmans, Robert J and Guisan, Antoine and Peterson, A Townsend and Loiselle, Bette A and {The Nceas Predicting Species Distribution Working Group}},
doi = {10.1111/j.1365-2664.2007.01408.x},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2008{\_}Graham et al.{\_}Journal of Applied Ecology.pdf:pdf},
journal = {J Appl Ecol},
pages = {239--247},
title = {{The influence of spatial errors in species occurrence data used in distribution models}},
volume = {45},
year = {2008}
}
@article{Graham2008,
author = {Graham, Catherine H and Elith, Jane and Hijmans, Robert J and Guisan, Antoine and Peterson, A Townsend and Loiselle, Bette A and {The Nceas Predicting Species Distribution Working Group}},
doi = {10.1111/j.1365-2664.2007.01408.x},
journal = {J Appl Ecol},
pages = {239--247},
title = {{The influence of spatial errors in species occurrence data used in distribution models}},
volume = {45},
year = {2008}
}
@article{Gratton2017,
abstract = {Aim Comparative phylogeography across a large number of species allows investigating community-level processes at regional and continental scales. An effective approach to such studies would involve automatic retrieval of georeferenced sequence data from nucleotide databases (a first step towards an ‘automated phylogeography'). It remains unclear if, despite repeated calls, georeferencing of nucleotide databases has increased in frequency, and if accumulated data allow for broad applications based on automated retrieval of sequence data and associated geographical information. Here, we investigated geographical information available in NCBI GenBank accessions for tetrapods, exploring temporal and geographical patterns in georeferencing, and quantifying data available for automated phylogeography. Location Global. Methods We developed Python and R scripts to (1) download metadata from GenBank (1,125,514 accessions, {\textgreater} 20,000 species); (2) geocode accessions from associated metadata; (3) map originally georeferenced and geocoded accessions and plot their frequency against time; (4) assess the size of intraspecific sets of homologous sequences and compare their geographical extent with species ranges, thus evaluating their potential for phylogeographical analyses. Results Only 6.2{\%} of surveyed tetrapod GenBank submissions reported geographical coordinates, without increase in recent years. Our geocoding raised georeferenced accessions to 15.1{\%}. The geographical distribution of georeferenced accessions is patchy, and especially sparse in economically underdeveloped areas. Automatically retrievable informative data sets covering most of the range are available for very few species of wide-ranging tetrapods. Main conclusions Although geocoding offers a partial solution to the scarcity of direct georeferencing, the amount of data potentially useful for automated phylogeography is still limited. Strong underrepresentation of hard-to-access areas suggests that sampling logistics represent a main hindrance to global data availability. We propose that, besides enhancing georeferencing of genetic data, future research agendas should focus on collaborative efforts to sample genetic diversity in biodiversity-rich tropical areas.},
author = {Gratton, Paolo and Marta, Silvio and Bocksberger, Ga{\"{e}}lle and Winter, Marten and Trucchi, Emiliano and K{\"{u}}hl, Hjalmar},
doi = {10.1111/jbi.12786},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2017{\_}Gratton et al.{\_}Journal of Biogeography.pdf:pdf},
isbn = {1365-2699},
issn = {13652699},
journal = {J Biogeogr},
keywords = {DNA barcoding,GenBank,biodiversity,comparative phylogeography,geodata,georeferencing,metadata},
number = {2},
pages = {475--486},
title = {{A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography?}},
volume = {44},
year = {2017}
}
@article{Gratton2017,
abstract = {Aim Comparative phylogeography across a large number of species allows investigating community-level processes at regional and continental scales. An effective approach to such studies would involve automatic retrieval of georeferenced sequence data from nucleotide databases (a first step towards an ‘automated phylogeography'). It remains unclear if, despite repeated calls, georeferencing of nucleotide databases has increased in frequency, and if accumulated data allow for broad applications based on automated retrieval of sequence data and associated geographical information. Here, we investigated geographical information available in NCBI GenBank accessions for tetrapods, exploring temporal and geographical patterns in georeferencing, and quantifying data available for automated phylogeography. Location Global. Methods We developed Python and R scripts to (1) download metadata from GenBank (1,125,514 accessions, {\textgreater}20,000 species); (2) geocode accessions from associated metadata; (3) map originally georeferenced and geocoded accessions and plot their frequency against time; (4) assess the size of intraspecific sets of homologous sequences and compare their geographical extent with species ranges, thus evaluating their potential for phylogeographical analyses. Results Only 6.2{\%} of surveyed tetrapod GenBank submissions reported geographical coordinates, without increase in recent years. Our geocoding raised georeferenced accessions to 15.1{\%}. The geographical distribution of georeferenced accessions is patchy, and especially sparse in economically underdeveloped areas. Automatically retrievable informative data sets covering most of the range are available for very few species of wide-ranging tetrapods. Main conclusions Although geocoding offers a partial solution to the scarcity of direct georeferencing, the amount of data potentially useful for automated phylogeography is still limited. Strong underrepresentation of hard-to-access areas suggests that sampling logistics represent a main hindrance to global data availability. We propose that, besides enhancing georeferencing of genetic data, future research agendas should focus on collaborative efforts to sample genetic diversity in biodiversity-rich tropical areas.},
author = {Gratton, Paolo and Marta, Silvio and Bocksberger, Ga{\"{e}}lle and Winter, Marten and Trucchi, Emiliano and K{\"{u}}hl, Hjalmar},
doi = {10.1111/jbi.12786},
isbn = {1365-2699},
issn = {13652699},
journal = {J Biogeogr},
keywords = {DNA barcoding,GenBank,biodiversity,comparative phylogeography,geodata,georeferencing,metadata},
number = {2},
pages = {475--486},
title = {{A world of sequences: can we use georeferenced nucleotide databases for a robust automated phylogeography?}},
volume = {44},
year = {2017}
}
@article{Gueta2016,
abstract = {The recent availability of species occurrence data from numerous sources, standardized and connected within a single portal, has the potential to answer fundamental ecological questions. These aggregated big biodiversity databases are prone to numerous data errors and biases. The data-user is responsible for identifying these errors and assessing if the data are suitable for a given purpose. Complex technical skills are increasingly required for handling and cleaning biodiversity data, while biodiversity scientists possessing these skills are rare. Here, we estimate the effect of user-level data cleaning on species distribution model (SDM) performance. We implement several simple and easy-to-execute data cleaning procedures, and evaluate the change in SDM performance. Additionally, we examine if a certain group of species is more sensitive to the use of erroneous or unsuitable data. The cleaning procedures used in this research improved SDM performance significantly, across all scales and for all performance measures. The largest improvement in distribution models following data cleaning was for small mammals (1 g-100 g). Data cleaning at the user level is crucial when using aggregated occurrence data, and facilitating its implementation is a key factor in order to advance data-intensive biodiversity studies. Adopting a more comprehensive approach for incorporating data cleaning as part of data analysis, will not only improve the quality of biodiversity data, but will also impose a more appropriate usage of such data.},
author = {Gueta, Tomer and Carmel, Yohay},
doi = {10.1016/j.ecoinf.2016.06.001},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2016{\_}Gueta, Carmel{\_}Ecological Informatics.pdf:pdf},
issn = {15749541},
journal = {Ecol Inform},
keywords = {Australian mammals,Big-data,Biodiversity informatics,Data-cleaning,MaxEnt,SDM performance,biodiversity informatics},
pages = {139--145},
publisher = {Elsevier B.V.},
title = {{Quantifying the value of user-level data cleaning for big data: A case study using mammal distribution models}},
volume = {34},
year = {2016}
}
@article{Guo2017,
author = {Guo, Q and Liu, Y and Wieczorek, J},
doi = {10.1080/13658810701851420},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2017{\_}Guo, Liu, Wieczorek{\_}Geographic Information Science.pdf:pdf},
journal = {Geogr Inf Sci},
number = {10},
title = {{Georeferencing locality descriptions and computing associated uncertainty using a probabilistic approach}},
volume = {8816},
year = {2017}
}
@article{Guo2017,
author = {Guo, Q and Liu, Y and Wieczorek, J},
doi = {10.1080/13658810701851420},
journal = {Geogr Inf Sci},
number = {10},
title = {{Georeferencing locality descriptions and computing associated uncertainty using a probabilistic approach}},
volume = {8816},
year = {2017}
}
@manual{Hester2017,
annote = {R package version 3.0.1},
author = {Hester, Jim},
title = {{covr: Test Coverage for Packages}},
url = {https://cran.r-project.org/package=covr},
year = {2017}
}
@manual{Hijmans2016a,
annote = {R package version 1.5-5},
author = {Hijmans, Robert J},
title = {{geosphere: Spherical Trigonometry}},
url = {https://cran.r-project.org/package=geosphere},
year = {2016}
}
@manual{Hijmans2016,
annote = {R package version 2.5-8},
author = {Hijmans, Robert J},
title = {{raster: Geographic Data Analysis and Modeling}},
url = {https://cran.r-project.org/package=raster},
year = {2016}
}
@manual{Hijmans2017a,
annote = {R package version 2.6-7},
author = {Hijmans, Robert J},
title = {{raster: Geographic Data Analysis and Modeling}},
url = {https://cran.r-project.org/package=raster},
year = {2017}
}
@manual{Hijmans2017,
annote = {R package version 1.5-7},
author = {Hijmans, Robert J},
title = {{geosphere: Spherical Trigonometry}},
url = {https://cran.r-project.org/package=geosphere},
year = {2017}
}
@misc{IndexHerbariorum2017,
author = {{Index Herbariorum}},
title = {{http://sciweb.nybg.org/Science2/IndexHerbariorum.asp}},
year = {2017}
}
@article{Johnson2007,
author = {Johnson, Chris J and Gillingham, Michael P},
doi = {10.1016/j.ecolmodel.2007.11.013},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2008{\_}Johnson, Gillingham{\_}Ecological Modelling.pdf:pdf},
journal = {Ecol Modell},
pages = {143--155},
title = {{Sensitivity of species-distribution models to error, bias, and model design: An application to resource selection functions for woodland caribou}},
volume = {3},
year = {2008}
}
@article{Johnson2007,
author = {Johnson, Chris J and Gillingham, Michael P},
doi = {10.1016/j.ecolmodel.2007.11.013},
journal = {Ecol Model},
pages = {143--155},
title = {{Sensitivity of species-distribution models to error, bias, and model design: An application to resource selection functions for woodland caribou}},
volume = {3},
year = {2008}
}
@article{Kahle2013,
author = {Kahle, David and Wickham, Hadley},
journal = {R J},
number = {1},
pages = {144--161},
title = {{ggmap: Spatial Visualization with ggplot2}},
url = {http://journal.r-project.org/archive/2013-1/kahle-wickham.pdf},
volume = {5},
year = {2013}
}
@article{Maldonado2015,
author = {Maldonado, Carla and Molina, Carlos I. and Zizka, Alexander and Persson, Claes and Taylor, Charlotte M. and Alb{\'{a}}n, Joaquina and Chilquillo, Eder and R{\o}nsted, Nina and Antonelli, Alexandre},
doi = {10.1111/geb.12326},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature//2015{\_}Maldonado et al.{\_}Global Ecology and Biogeography.pdf:pdf},
issn = {1466822X},
journal = {Glob Ecol Biogeogr},
keywords = {cinchoneae,data quality,gbif,occurrence data,rubiaceae,species richness},
number = {8},
pages = {973--984},
title = {{Estimating species diversity and distribution in the era of Big Data: To what extent can we trust public databases}},
volume = {24},
year = {2015}
}
@article{Mathew2014,
author = {Mathew, Cherian and G{\"{u}}ntsch, Anton and Obst, Matthias and Vicario, Saverio and Haines, Robert and Williams, ALan R and de Jong, Yde and Goble, Carole},
doi = {10.3897/BDJ.2.e4221},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2014{\_}Mathew et al.{\_}Biodiversity Data Journal.pdf:pdf},
journal = {Biodivers Data J},
keywords = {biodiversity informatics,data,service oriented architecture,web services,workflows},
pages = {e4221},
title = {{A semi-automated workflow for biodiversity data retrieval, cleaning, and quality control}},
volume = {2},
year = {2014}
}
@misc{IndexHerbariorum2017,
author = {{New York Botanical Garden}},
title = {{Index Herbariorum}},
url = {http://sciweb.nybg.org/Science2/IndexHerbariorum.asp},
urldate = {2017-11-20},
year = {2017}
}
@misc{PBDB2018,
author = {PBDB},
publisher = {Paleobiology database},
title = {{The data were downloaded from the Paleobiology Database on on 26 January 2018, using the group names magnoliophyta, magnoliopsida, angiospermae}},
url = {www.paleobiodb.org},
year = {2018}
}
@article{Pebesma2005,
author = {Pebesma, E.J. and Bivand, R.S.},
journal = {R News},
number = {2},
title = {{Classes and methods for spatial data in R.}},
url = {https://cran.r-project.org/doc/Rnews/},
volume = {5},
year = {2005}
}
@misc{QGISDevelopmentTeam2017,
author = {{QGIS Development Team}},
title = {{QGIS Geographic Information System. Open Source Geospatial Foundation Project.}},
url = {www.qgis.org},
year = {2017}
}
@manual{RCoreTeam2017,
address = {Vienna, Austria},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
title = {{R: A Language and Environment for Statistical Computing}},
url = {https://www.r-project.org/},
year = {2018}
}
@manual{Becker2017,
annote = {R package version 3.2.0},
author = {{Richard A. Becker} and Brownrigg, Ray and Minka, Thomas P and R, Allan R Wilks. and Deckmyn, Alex},
title = {{maps: Draw Geographical Maps}},
url = {https://cran.r-project.org/package=maps},
year = {2017}
}
@article{Robertson2010,
author = {Robertson, M P and Cumming, G S and Erasmus, B F N},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2010{\_}Robertson, Cumming, Erasmus{\_}Diversity and Distributions(2).pdf:pdf},
journal = {Divers Distrib},
keywords = {atlas projects,biodiversity databases,conservation biogeography,data quality},
pages = {363--375},
title = {{Getting the most out of atlas data}},
volume = {16},
year = {2010}
}
@article{Robertson2016,
author = {Robertson, Mark P and Visser, Vernon and Hui, Cang},
doi = {10.1111/ecog.02118},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2016{\_}Robertson, Visser, Hui{\_}Ecography.pdf:pdf},
journal = {Ecography (Cop)},
pages = {394--401},
title = {{Biogeo: an R package for assessing and improving data quality of occurrence record datasets}},
volume = {39},
year = {2016}
}
@article{Robertson2016,
author = {Robertson, Mark P and Visser, Vernon and Hui, Cang},
doi = {10.1111/ecog.02118},
journal = {Ecography (Cop)},
pages = {394--401},
title = {{Biogeo: an R package for assessing and improving data quality of occurrence record datasets}},
volume = {39},
year = {2016}
}
@article{Wilson2006,
author = {Rondinini, Carlo and Wilson, Kerrie A and Boitani, Luigi and Grantham, HEdley and {Hugh P Possingham}},
doi = {10.1111/j.1461-0248.2006.00970.x},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2006{\_}Rondinini et al.{\_}Ecology Letters.pdf:pdf},
journal = {Ecol Lett},
keywords = {1136,1145,2006,9,commission error,data,ecology letters,geographic range,omission error,point data,predicted distribution,reserve selection},
pages = {1136--1145},
title = {{Tradeoffs of different types of species occurrence data for use in systematic conservation planning}},
volume = {9},
year = {2006}
}
@article{Wilson2006,
author = {Rondinini, Carlo and Wilson, Kerrie A and Boitani, Luigi and Grantham, HEdley and {Hugh P Possingham}},
doi = {10.1111/j.1461-0248.2006.00970.x},
journal = {Ecol Lett},
keywords = {1136,1145,2006,9,commission error,data,ecology letters,geographic range,omission error,point data,predicted distribution,reserve selection},
pages = {1136--1145},
title = {{Tradeoffs of different types of species occurrence data for use in systematic conservation planning}},
volume = {9},
year = {2006}
}
@manual{Salmon2017,
annote = {R package version 0.1.2},
author = {Salmon, Ma{\"{e}}lle},
title = {{opencage: Interface to the OpenCage API}},
url = {https://cran.r-project.org/package=opencage},
year = {2017}
}
@article{Silvestro2014,
author = {Silvestro, Daniele and Salamin, Nicolas and Schnitzler, Jan},
doi = {10.1111/2041-210X.12263},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2014{\_}Silvestro, Salamin, Schnitzler{\_}Methods in Ecology and Evolution.pdf:pdf},
journal = {Methods Ecol Evol},
pages = {1126--1131},
title = {{PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data}},
volume = {5},
year = {2014}
}
@article{Silvestro2014,
author = {Silvestro, Daniele and Salamin, Nicolas and Schnitzler, Jan},
doi = {10.1111/2041-210X.12263},
journal = {Methods Ecol Evol},
pages = {1126--1131},
title = {{PyRate: a new program to estimate speciation and extinction rates from incomplete fossil data}},
volume = {5},
year = {2014}
}
@manual{South,
annote = {R package version 0.1.0},
author = {South, Andy},
title = {{rnaturalearth: World Map Data from Natural Earth}},
url = {https://github.com/ropenscilabs/rnaturalearth},
year = {2017}
}
@misc{BotanicalInformationandEcologyNetwork2015,
author = {{The Botanical Information and Ecology Network}},
booktitle = {Publ Internet},
title = {{BIEN3, http://bien.nceas.ucsb.edu/bien/}},
urldate = {2015-03-01},
year = {2015}
}
@misc{TheGlobalRegistryofBiodiversityRepositories2017,
author = {{The Global Registry of Biodiversity Repositories}},
title = {www.grbio.org},
url = {www.grbio.org},
urldate = {2016-11-20},
year = {2017}
}
@misc{TheGlobalRegistryofBiodiversityRepositories2017,
author = {{The Global Registry of Biodiversity Repositories}},
title = {www.grbio.org},
year = {2017}
}
@misc{TheGlobalRegistryofBiodiversityRepositories2017,
author = {{The Global Registry of Biodiversity Repositories}},
title = {www.grbio.org},
url = {www.grbio.org},
year = {2017}
}
@article{Topel2017,
author = {T{\"{o}}pel, Mats and Zizka, Alexander and Cali{\'{o}}, Maria Fernanda and Scharn, Ruud and Silvestro, Daniele and Antonelli, Alexandre and Calio, M F and Scharn, Ruud and Silvestro, Daniele and Antonelli, Alexandre},
doi = {10.1093/sysbio/syw064},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature//2014{\_}T{\"{o}}pel et al.{\_}bioRxiv.10.1101009274.10.1101009274.pdf:pdf;:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2017{\_}T{\"{o}}pel et al.{\_}Systematic biology.pdf:pdf},
journal = {Syst Biol},
number = {2},
pages = {145--151},
title = {{SpeciesGeoCoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology, and evolution}},
volume = {66},
year = {2017}
}
@misc{UNEP-WCMCandIUCN2017,
author = {{UNEP-WCMC and IUCN}},
booktitle = {Cambridge, UK UNEP-WCMC IUCN},
title = {{Protected Planet; The World Database on Protected Areas (WDPA)/The Global Database on Protected Areas Management Effectiveness (GD-PAME) [on-line],[Jun 2017]. Available at www.protectedplanet.net}},
year = {2017}
}
@manual{Varela2016,
annote = {R package version 0.5.0},
author = {Varela, Sara and {Gonzalez Hernandez}, Javier and {Fabris Sgarbi}, Luciano},
title = {{paleobioDB: Download and Process Data from the Paleobiology Database}},
url = {https://cran.r-project.org/package=paleobioDB},
year = {2016}
}
@article{Varela2011,
abstract = {The increasing interest in the effects of climate changes on species distributions has been followed by the development of Species Distribution Models (SDMs). Although these techniques are starting to be used to study the location and dynamics of past species distributions, a sound theoretical framework for their use in paleoecology is still lacking. In this paper we are reviewing the main challenges for constructing Paleo-Species Distribution Models to describe and project the past distribution of species, namely data limitations, selection of predictors and choice of a biologically-relevant modeling procedure. We also review and discuss the current state-of-the-art in Paleo-SDMs, providing a series of recommendations for their use, and proposing future research lines to improve the use of these techniques in paleobiogeography. {\textcopyright} 2011 Elsevier B.V.},
author = {Varela, Sara and Lobo, Jorge M. and Hortal, Joaqu{\'{i}}n},
doi = {10.1016/j.palaeo.2011.07.021},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2011{\_}Varela, Lobo, Hortal{\_}Palaeogeography, Palaeoclimatology, Palaeoecology.pdf:pdf},
isbn = {00310182},
issn = {00310182},
journal = {Palaeogeogr Palaeoclimatol Palaeoecol},
keywords = {Bias in occurrence data,Biodiversity databases,Biogeography,Extinction,Fossil record,Geographic range dynamics,Grinnellian niche,Scenopoetic variables,Uncertainty},
number = {3-4},
pages = {451--463},
publisher = {Elsevier B.V.},
title = {{Using species distribution models in paleobiogeography: A matter of data, predictors and concepts}},
url = {http://dx.doi.org/10.1016/j.palaeo.2011.07.021},
volume = {310},
year = {2011}
}
@book{Wickham2009,
abstract = {Use R!},
address = {New York},
author = {Wickham, Hadley},
booktitle = {Springer},
doi = {10.1007/978-0-387-98141-3},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2009{\_}Wickham{\_}Springer.pdf:pdf},
isbn = {9780387981406},
issn = {10184619},
pages = {222},
pmid = {19791908},
publisher = {Springer},
title = {{ggplot2 - Elegant Graphics for Data Analysis}},
year = {2009}
}
@book{Wickham2016,
author = {Wickham, Hadley},
isbn = {978-3-319-24277-4},
publisher = {Springer-Verlag New York},
title = {{ggplot2: Elegant Graphics for Data Analysis}},
url = {http://ggplot2.org},
year = {2016}
}
@article{Wickham2011,
author = {Wickham, Hadley},
journal = {R J},
pages = {5--10},
title = {{testthat: Get Started with Testing}},
url = {https://journal.r-project.org/archive/2011-1/RJournal{\_}2011-1{\_}Wickham.pdf},
volume = {3},
year = {2011}
}
@manual{Wickham2017,
annote = {R package version 6.0.1},
author = {Wickham, Hadley and Danenberg, Peter and Eugster, Manuel},
title = {{roxygen2: In-Line Documentation for R}},
url = {https://cran.r-project.org/package=roxygen2},
year = {2017}
}
@manual{Wickham2018,
annote = {R package version 1.1.0},
author = {Wickham, Hadley and Hesselberth, Jay},
title = {{pkgdown: Make Static HTML Documentation for a Package}},
url = {https://cran.r-project.org/package=pkgdown},
year = {2018}
}
@manual{Wickham2018a,
annote = {R package version 1.13.6},
author = {Wickham, Hadley and Hester, Jim and Chang, Winston},
title = {{devtools: Tools to Make Developing R Packages Easier}},
url = {https://cran.r-project.org/package=devtools},
year = {2018}
}
@misc{Wikipedia2017,
author = {Wikipedia},
title = {{List of zoos by country}},
url = {https://en.wikipedia.org/wiki/List{\_}of{\_}zoos{\_}by{\_}country},
urldate = {2016-11-20},
year = {2017}
}
@manual{Xie2018,
annote = {R package version 1.20},
author = {Xie, Yihui},
title = {{knitr: A General-Purpose Package for Dynamic Report Generation in R}},
url = {https://yihui.name/knitr/},
year = {2018}
}
@article{Yesson2007,
author = {Yesson, Chris and Brewer, Peter W and Sutton, Tim and Caithness, Neil and Pahwa, Jaspreet S and Burgess, Mikhaila and Gray, W Alec and White, Richard J and Andrew, C and Bisby, Frank A and Culham, Alastair},
doi = {10.1371/journal.pone.0001124},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2007{\_}Yesson et al.{\_}PLoSone.PDF:PDF},
journal = {PLoSone},
pages = {e1124},
title = {{How Global Is the Global Biodiversity Information Facility?}},
volume = {11},
year = {2007}
}
@article{Yesson2007,
author = {Yesson, Chris and Brewer, Peter W and Sutton, Tim and Caithness, Neil and Pahwa, Jaspreet S and Burgess, Mikhaila and Gray, W Alec and White, Richard J and Andrew, C and Bisby, Frank A and Culham, Alastair},
doi = {10.1371/journal.pone.0001124},
journal = {PLoSone},
pages = {e1124},
title = {{How Global Is the Global Biodiversity Information Facility?}},
volume = {11},
year = {2007}
}
@article{Zanne2014,
abstract = {Early flowering plants are thought to have been woody species restricted to warm habitats. This lineage has since radiated into almost every climate, with manifold growth forms. As angiosperms spread and climate changed, they evolved mechanisms to cope with episodic freezing. To explore the evolution of traits underpinning the ability to persist in freezing conditions, we assembled a large species-level database of growth habit (woody or herbaceous; 49,064 species), as well as leaf phenology (evergreen or deciduous), diameter of hydraulic conduits (that is, xylem vessels and tracheids) and climate occupancies (exposure to freezing). To model the evolution of species' traits and climate occupancies, we combined these data with an unparalleled dated molecular phylogeny (32,223 species) for land plants. Here we show that woody clades successfully moved into freezing-prone environments by either possessing transport networks of small safe conduits and/or shutting down hydraulic function by dropping leaves during freezing. Herbaceous species largely avoided freezing periods by senescing cheaply constructed aboveground tissue. Growth habit has long been considered labile, but we find that growth habit was less labile than climate occupancy. Additionally, freezing environments were largely filled by lineages that had already become herbs or, when remaining woody, already had small conduits (that is, the trait evolved before the climate occupancy). By contrast, most deciduous woody lineages had an evolutionary shift to seasonally shedding their leaves only after exposure to freezing (that is, the climate occupancy evolved before the trait). For angiosperms to inhabit novel cold environments they had to gain new structural and functional trait solutions; our results suggest that many of these solutions were probably acquired before their foray into the cold.},
author = {Zanne, Amy E and Tank, David C and Cornwell, William K and Eastman, Jonathan M and Smith, Stephen a and FitzJohn, Richard G and McGlinn, Daniel J and O'Meara, Brian C and Moles, Angela T and Reich, Peter B and Royer, Dana L and Soltis, Douglas E and Stevens, Peter F and Westoby, Mark and Wright, Ian J and Aarssen, Lonnie and Bertin, Robert I and Calaminus, Andre and Govaerts, Rafa{\"{e}}l and Hemmings, Frank and Leishman, Michelle R and Oleksyn, Jacek and Soltis, Pamela S and Swenson, Nathan G and Warman, Laura and Beaulieu, Jeremy M},
doi = {10.1038/nature12872},
file = {:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature//2014{\_}Zanne et al.{\_}Nature.pdf:pdf;:C$\backslash$:/Users/alexander.zizka/Dropbox (Antonelli Lab)/Arbeit/Literature/2014{\_}Zanne et al.{\_}Nature(2).pdf:pdf},
issn = {1476-4687},
journal = {Nature},
keywords = {Angiosperms,Angiosperms: anatomy {\&} histology,Angiosperms: physiology,Biological Evolution,Cold Climate,Ecosystem,Freezing,Likelihood Functions,Phylogeography,Plant Leaves,Plant Leaves: anatomy {\&} histology,Plant Leaves: physiology,Seeds,Seeds: physiology,Time Factors,Wood,Wood: anatomy {\&} histology,Wood: physiology,Xylem,Xylem: anatomy {\&} histology,Xylem: physiology},
number = {7486},
pages = {89--92},
pmid = {24362564},
title = {{Three keys to the radiation of angiosperms into freezing environments.}},
volume = {506},
year = {2014}
}
